Yip Yew Mun

json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

1

I tried running of the notebooks (REINVENT_Use-Case-DRD2_demo). When I was trying to execute python input.py DRD2_config.json, it gave the error: json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0) What...

Substituting energy value from external calculation into openmm for coordinates generation

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Hi, I would like to know where in the code can I substitute the energy value obtained from external software calculation, and use that in OpenMM for forces computation and...

Enquiring about running TIES MD for protein-ligand complex

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Hi, I was trying to run TIES MD for protein ligand complex, but sadly I couldn't find any tutorials online to help me with it. Could someone guide me on...

KeyError: 'speaker_embedding' and TypeError: Log._log() got an unexpected keyword argument 'exc_info'

1

Hi, I encountered the following error, could someone help me? Python 3.10.12 | packaged by conda-forge | (main, Jun 23 2023, 22:40:32) [GCC 12.3.0] on linux Type "help", "copyright", "credits"...

Hi! I was looking at the `HDBSCAN_Chemoinfo.ipynb` in the `chemicalspace2` folder and I saw these 2 blocks of code: ``` import numba @numba.njit() def tanimoto_dist(a,b): dotprod = np.dot(a,b) tc =...

Hi, I'm interested to use FAST to do protein-ligand binding prediction, however when I looked at the scripts, they are all referenced to "/p/lscratchh/jones289/data/" which is not found in the...

I was running run_test.py and I encountered: ValueError: Found array with 0 feature(s) (shape=(1, 0)) while a minimum of 1 is required by check_pairwise_arrays.

Unable to run inference

9

Hi, I was trying to run the following command `neuralplexer-inference --task=batched_structure_sampling --input-receptor DERETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIPLFYMELALGQHNRKGAITCWGRLVPLFKGIGYAVVLIAFYVDFYYNVIIAWSLRFFFASFTNSLPWTSCNNIWNTPNCRPFEGHVEGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALCLLIVYLICYFSLWKGISTSGKVVWFTALFPYAVLLILLIRGLTLPGSFLGIQYYLTPNFSAIYKAEVWVDAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFVIFSVLGYMAHTLGVRIEDVATEGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSSFGGSEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYSILVAVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYGLIGYEPLTYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQRFTILTTPWRDQQ --input-ligand 41X_model_ed.sdf --out-path test_4xnx_41x --model-checkpoint ./complex_structure_prediction.ckpt --n-samples 16 --chunk-size 4 --num-steps=40 --sampler=langevin_simulated_annealing --cuda` and I got the...

[Question]: If I shut down the OS, what is the docker command to run so that I don't have to reinstall the OS right from the start again?

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### Is your question not already answered in the FAQ? - [X] I made sure the question is not listed in the [FAQ](https://github.com/dockur/macos/blob/master/readme.md). ### Is this a general question and...